External Email - Use Caution
Hi Thank you for your response, here is the terminal output: It does create a new annot, but it's empty.
bw Michal
cwd /Applications/freesurfer/subjects/Alldata6V/bert cmdline mris_label2annot --s bert --h lh --ctab label/aparc.annot.a2009s.ctab --a myaprac11 --l dir/lh.G_insular_short.label --l dir/lh.G_Ins_lg&S_cent_ins.label --debug
subject bert hemi lh SUBJECTS_DIR /Applications/freesurfer/subjects/Alldata6V ColorTable label/aparc.annot.a2009s.ctab AnnotName myaprac11 nlables 2 LabelThresh 0 0.000000 Loading /Applications/freesurfer/subjects/Alldata6V/bert/surf/lh.orig 1 -1 NOT_FOUND 2 -1 NOT_FOUND Mapping unhit to unknown Found 131576 unhit vertices
On Mon, 20 May 2019 at 20:11, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: mkanalysis-sess refeventdur (Greve, Douglas N.,Ph.D.)
- Re: MP-RAGE protocol (Greve, Douglas N.,Ph.D.)
- Re: Question about recon-all.v6.hires (Greve, Douglas N.,Ph.D.)
- Re: mkanalysis-sess refeventdur (Nasiriavanaki, Zahra)
- problem with mri_surfcluster (Barletta, Valeria)
- Re: problem with mri_surfcluster (Greve, Douglas N.,Ph.D.)
- Re: mris_label2annot empty Annot (Greve, Douglas N.,Ph.D.)
- Re: problem with mri_surfcluster (Barletta, Valeria)
- Re: Fixing of Morphometry Stats and Global Measure of Volume: Longitudinal analysis (Greve, Douglas N.,Ph.D.)
- Re: problem with mri_surfcluster (Greve, Douglas N.,Ph.D.)
- Re: problem with mri_surfcluster (Barletta, Valeria)
Message: 1 Date: Mon, 20 May 2019 16:52:39 +0000 From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] mkanalysis-sess refeventdur To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 4f503934-d973-7563-2a14-235cb86012c6@mgh.harvard.edu Content-Type: text/plain; charset="Windows-1252"
No, you'll need to change your paradigm file to have two distinct 8 sec events rather than one 16 sec event.
On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote:
Hi Freesurfer experts
I am?making an analysis in Freesurfer version 6 and?I have a question about the "refeventdur" in mkanalysis-sess command.
My stimulus duration is 16 seconds, but for a specific analysis, I only want to include half of the stimulus duration (ex:?the?first 8 seconds only OR the?last 8 seconds only).
I was wondering if I can do this, by setting the "refeventdur" to 8 seconds.? Will that work? and if it does, is it including the first 8 seconds or the last 8 seconds?
Thanks
Mona
*Zahra?(Mona) Nasiriavanaki*
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 2 Date: Mon, 20 May 2019 16:55:39 +0000 From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] MP-RAGE protocol To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: e482d81c-774b-00ea-a70e-809139c87bb5@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Your attachment says that none of the commands could be found. Make sure you set up your environment correctly
On 5/20/19 4:53 AM, mustafa amin wrote:
????????External Email - Use Caution
Hi Bruce,
Thank you for your swift response as always, may I know how to convert the more than 100 DICOM files to mgz or nifti? I noticed that the command is for 1 file/image, please correct me if I am wrong. The MP-RAGE file that I sent you is more than 50 images.
I tried to follow your instruction however it did not work smoothly. The diacom files couldn't be converted to mgz. I have attached the command that still did not work when I used them in this email. Please have a look and share some thoughts. Thank you for your kind attention and cooperation.
Pada Jumat, 17 Mei 2019 21.14.44 WIB, Bruce Fischl fischl@nmr.mgh.harvard.edu menulis:
Hi Mustafa
- Your mprage ran through recon-all fine and the results look good. The
saggital field of view is tight, so make sure that they don't crop brain in that direction.
- Your recon-all command line is incorrect. You should point the
SUBJECTS_DIR environment variable to whereever you want to store all of your FreeSurfer-processed data, then use the -i switch to path to the input volume. You can also specify SUBJECTS_DIR on the command line. So in your case something like:
recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 -sd \ ??? ? /path/to/my/subjecs -all
should do the trick. There is also no need to convert to nifti first
cheers Bruce
On Fri, 17 May 2019, mustafa amin wrote:
????????External Email - Use Caution
Hi Bruce,
Herewith I attach within the email the command that didn't work when
I wanted to reconall. Please
have a look. What about the previous dicom that I have sent to you?
Please share some thoughts.Thank
you very much.
Yours faithfully,
Mustafa
Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl
<fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
menulis:
Hi Mustafa
can you give us some detials? What didn't work? Can you send us the
full
command line, screen output and recon-all.log?
cheers Bruce
On Thu, 16 May 2019, mustafa amin wrote:
????????External Email - Use Caution
Hi Douglas,
I tried to follow the instruction to recon-all the data however it
didn't work. Please give
some thoughts. Thank you in advance.
Yours faithfully,
Mustafa
Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D.
<DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>
menulis:
Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
? ? ? ? ? External Email - Use Caution
Hi Bruce,
I?ve talked to the MRI operator and she told me that the best
thing to do the MP-RAGE
protocol is doing the T1 weighted 3D gradient echo with SENSE, she
can?t set the TE, TR, TI
just like the ADNI protocol asked, though. She can set the
thickness to 1 mm. Is this set
up okay?
I have the DIACOM files of some subjects with the set up above.
Can I send them to you to
look at them?
? I am terribly sorry for keep asking this basic question due to
we never had experience
doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl
<fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up
in an
astonishing number of ways. By far the best thing to do would
be to acquire
a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to
acquire one
and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
>? ? ? ? External Email - Use Caution > > Dear Freesurfer experts, > > I need advice, the MRI operator need to confirm whether she
had done the
> right protocol of MP-RAGE. I have attached the picture that
has been
> taken by her. Please share some thoughts. Thank you in advance. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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Message: 3 Date: Mon, 20 May 2019 16:59:08 +0000 From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] Question about recon-all.v6.hires To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: c6c9e090-4ae9-1307-aad4-ac0822b1eed3@mgh.harvard.edu Content-Type: text/plain; charset="Windows-1252"
They should be there. Can you send recon-all.log and conf2hires.log files?
On 5/20/19 9:59 AM, Bruce Fischl wrote:
Hi Victor
the lh.white.{KH} are generated from the lh.white file, so I don't think it can have skipped creating it. Was it deleted? Can you double check?
Bruce On Mon, 20 May 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
Hi all,
I am running 7T scans through FS6, and I have been recommended to install the tools in?
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/
. So I ran the new recon-all.v6.hires, specifically with the command "recon-all.hires.v6 -s subj -conf2hires -all"
For the most part, it ran, but I while QCing, it couldn't seem to load the surfs files. Recon-all seemed to have generated files called ?h.white.H and ?h.white.K, but apparently skipped the steps for ?h.white? I don't think I can load the surfs files without it, and I don't?know if this is intentional.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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Message: 4 Date: Mon, 20 May 2019 18:08:34 +0000 From: "Nasiriavanaki, Zahra" ZNASIRIAVANAKI@mgh.harvard.edu Subject: Re: [Freesurfer] mkanalysis-sess refeventdur To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: < DM6PR04MB44432A081ED580B5F392F5F199060@DM6PR04MB4443.namprd04.prod.outlook.com
Content-Type: text/plain; charset="us-ascii"
Got it.
Thank you very much for your reply
Mona
From: freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Monday, May 20, 2019 12:52:39 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mkanalysis-sess refeventdur
No, you'll need to change your paradigm file to have two distinct 8 sec events rather than one 16 sec event.
On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote:
Hi Freesurfer experts
I am making an analysis in Freesurfer version 6 and I have a question about the "refeventdur" in mkanalysis-sess command.
My stimulus duration is 16 seconds, but for a specific analysis, I only want to include half of the stimulus duration (ex: the first 8 seconds only OR the last 8 seconds only).
I was wondering if I can do this, by setting the "refeventdur" to 8 seconds. Will that work? and if it does, is it including the first 8 seconds or the last 8 seconds?
Thanks
Mona
*Zahra (Mona) Nasiriavanaki*
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I cannot replicate this. Can you look in the input labels and verify that they are not empty? Also, the "&" may be causing problems with the unix shell. Try using one that does not have an ampersand to see if it works.
On 5/21/19 4:31 AM, Michal Tanzer wrote:
External Email - Use Caution
Hi Thank you for your response, here is the terminal output: It does create a new annot, but it's empty.
bw Michal
cwd /Applications/freesurfer/subjects/Alldata6V/bert cmdline mris_label2annot --s bert --h lh --ctab label/aparc.annot.a2009s.ctab --a myaprac11 --l dir/lh.G_insular_short.label --l dir/lh.G_Ins_lg&S_cent_ins.label --debug
subject bert hemi lh SUBJECTS_DIR /Applications/freesurfer/subjects/Alldata6V ColorTable label/aparc.annot.a2009s.ctab AnnotName myaprac11 nlables 2 LabelThresh 0 0.000000 Loading /Applications/freesurfer/subjects/Alldata6V/bert/surf/lh.orig 1 -1 NOT_FOUND 2 -1 NOT_FOUND Mapping unhit to unknown Found 131576 unhit vertices
On Mon, 20 May 2019 at 20:11, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: mkanalysis-sess refeventdur (Greve, Douglas N.,Ph.D.) 2. Re: MP-RAGE protocol (Greve, Douglas N.,Ph.D.) 3. Re: Question about recon-all.v6.hires (Greve, Douglas N.,Ph.D.) 4. Re: mkanalysis-sess refeventdur (Nasiriavanaki, Zahra) 5. problem with mri_surfcluster (Barletta, Valeria) 6. Re: problem with mri_surfcluster (Greve, Douglas N.,Ph.D.) 7. Re: mris_label2annot empty Annot (Greve, Douglas N.,Ph.D.) 8. Re: problem with mri_surfcluster (Barletta, Valeria) 9. Re: Fixing of Morphometry Stats and Global Measure of Volume: Longitudinal analysis (Greve, Douglas N.,Ph.D.) 10. Re: problem with mri_surfcluster (Greve, Douglas N.,Ph.D.) 11. Re: problem with mri_surfcluster (Barletta, Valeria) ---------------------------------------------------------------------- Message: 1 Date: Mon, 20 May 2019 16:52:39 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] mkanalysis-sess refeventdur To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <4f503934-d973-7563-2a14-235cb86012c6@mgh.harvard.edu <mailto:4f503934-d973-7563-2a14-235cb86012c6@mgh.harvard.edu>> Content-Type: text/plain; charset="Windows-1252" No, you'll need to change your paradigm file to have two distinct 8 sec events rather than one 16 sec event. On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote: > > Hi Freesurfer experts > > > I am?making an analysis in Freesurfer version 6 and?I have a question > about the "refeventdur" in mkanalysis-sess command. > > My stimulus duration is 16 seconds, but for a specific analysis, I > only want to include half of the stimulus duration (ex:?the?first 8 > seconds only OR the?last 8 seconds only). > > I was wondering if I can do this, by setting the "refeventdur" to 8 > seconds.? Will that work? and if it does, is it including the first 8 > seconds or the last 8 seconds? > > > Thanks > > Mona > > > > *Zahra?(Mona) Nasiriavanaki* > > Postdoctoral Research Fellow > > Martinos Center for Biomedical Imaging > > Massachusetts General Hospital > > 149 13th Street, 149-2615 > > Charlestown, MA, USA, 02129 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 2 Date: Mon, 20 May 2019 16:55:39 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] MP-RAGE protocol To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <e482d81c-774b-00ea-a70e-809139c87bb5@mgh.harvard.edu <mailto:e482d81c-774b-00ea-a70e-809139c87bb5@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Your attachment says that none of the commands could be found. Make sure you set up your environment correctly On 5/20/19 4:53 AM, mustafa amin wrote: > > ????????External Email - Use Caution > > Hi Bruce, > > Thank you for your swift response as always, may I know how to convert > the more than 100 DICOM files to mgz or nifti? I noticed that the > command is for 1 file/image, please correct me if I am wrong. The > MP-RAGE file that I sent you is more than 50 images. > > I tried to follow your instruction however it did not work smoothly. > The diacom files couldn't be converted to mgz. I have attached the > command that still did not work when I used them in this email. Please > have a look and share some thoughts. Thank you for your kind attention > and cooperation. > > > Pada Jumat, 17 Mei 2019 21.14.44 WIB, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> menulis: > > > Hi Mustafa > > 1. Your mprage ran through recon-all fine and the results look good. The > saggital field of view is tight, so make sure that they don't crop > brain in > that direction. > > 2. Your recon-all command line is incorrect. You should point the > SUBJECTS_DIR environment variable to whereever you want to store all of > your FreeSurfer-processed data, then use the -i switch to path to the > input > volume. You can also specify SUBJECTS_DIR on the command line. So in your > case something like: > > > recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 > -sd \ > ??? ? /path/to/my/subjecs -all > > should do the trick. There is also no need to convert to nifti first > > cheers > Bruce > > > On Fri, > 17 May 2019, mustafa amin wrote: > > > > > ????????External Email - Use Caution > > > > > Hi Bruce, > > > > Herewith I attach within the email the command that didn't work when > I wanted to reconall. Please > > have a look. What about the previous dicom that I have sent to you? > Please share some thoughts.Thank > > you very much. > > > > Yours faithfully, > > > > Mustafa > > > > > > Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> menulis: > > > > > > Hi Mustafa > > > > can you give us some detials? What didn't work? Can you send us the full > > command line, screen output and recon-all.log? > > > > cheers > > Bruce > > > > > > On Thu, 16 May 2019, mustafa amin wrote: > > > > > > > > ????????External Email - Use Caution > > > > > > Hi Douglas, > > > > > > I tried to follow the instruction to recon-all the data however it > didn't work. Please give > > > some thoughts. Thank you in advance. > > > > > > Yours faithfully, > > > > > > Mustafa > > > > > > Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > menulis: > > > > > > > > > Hi Mustafa, why not just run recon-all on the data you have and see > > > whether it looks ok? > > > > > > On 4/15/19 7:06 AM, mustafa amin wrote: > > > >? ? ? ? ? External Email - Use Caution > > > > > > > > Hi Bruce, > > > > > > > > I?ve talked to the MRI operator and she told me that the best > thing to do the MP-RAGE > > > protocol is doing the T1 weighted 3D gradient echo with SENSE, she > can?t set the TE, TR, TI > > > just like the ADNI protocol asked, though. She can set the > thickness to 1 mm. Is this set > > > up okay? > > > > > > > > I have the DIACOM files of some subjects with the set up above. > Can I send them to you to > > > look at them? > > > > > > > >? I am terribly sorry for keep asking this basic question due to > we never had experience > > > doing it in Indonesia. > > > > > > > > Many thanks! > > > > > > > > > > > > Mustafa M. Amin > > > > Consultant Psychiatrist in Biological Psychiatry > > > > Department of Psychiatry > > > > Faculty of Medicine > > > > Universitas Sumatera Utara > > > > > > > >> On 2 Apr 2019, at 20.49, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > > >> > > > >> Hi Mustafa > > > >> > > > >> MRI is an amazingly versatile technology that can be messed up > in an > > > >> astonishing number of ways. By far the best thing to do would > be to acquire > > > >> a dataset and run it through recon-all and see if the results look > > > >> accurate. If you have permission to do so, you are welcome to > acquire one > > > >> and send it to us to try out instead. > > > >> > > > >> cheers > > > >> Bruce > > > >> > > > >> On Tue, 2 Apr 2019, mustafa amin > > > >> wrote: > > > >> > > > >>>? ? ? ? External Email - Use Caution > > > >>> > > > >>> Dear Freesurfer experts, > > > >>> > > > >>> I need advice, the MRI operator need to confirm whether she > had done the > > > >>> right protocol of MP-RAGE. I have attached the picture that > has been > > > >>> taken by her. Please share some thoughts. Thank you in advance. > > > >>> > > > >>> > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 3 Date: Mon, 20 May 2019 16:59:08 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] Question about recon-all.v6.hires To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <c6c9e090-4ae9-1307-aad4-ac0822b1eed3@mgh.harvard.edu <mailto:c6c9e090-4ae9-1307-aad4-ac0822b1eed3@mgh.harvard.edu>> Content-Type: text/plain; charset="Windows-1252" They should be there. Can you send recon-all.log and conf2hires.log files? On 5/20/19 9:59 AM, Bruce Fischl wrote: > Hi Victor > > the lh.white.{KH} are generated from the lh.white file, so I don't > think it can have skipped creating it. Was it deleted? Can you double > check? > > Bruce > On Mon, 20 May 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: > >> >> Hi all, >> >> >> I am running 7T scans through FS6, and I have been recommended to >> install the tools >> in?ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ >> . So I ran the new >> recon-all.v6.hires, specifically with the command "recon-all.hires.v6 >> -s subj -conf2hires -all" >> >> >> For the most part, it ran, but I while QCing, it couldn't seem to >> load the surfs files. Recon-all >> seemed to have generated files called ?h.white.H and ?h.white.K, but >> apparently skipped the steps >> for ?h.white? I don't think I can load the surfs files without it, >> and I don't?know if this is >> intentional. >> >> >> Victor Zeng >> Beth Israel Deaconess Medical Center >> Keshavan Lab >> -- >> >> ____________________________________________________________________________________________________ >> >> >> This message is intended for the use of the person(s) to whom it may >> be addressed. It may contain >> information that is privileged, confidential, or otherwise protected >> from disclosure under >> applicable law. If you are not the intended recipient, any >> dissemination, distribution, copying, or >> use of this information is prohibited. If you have received this >> message in error, please >> permanently delete it and immediately notify the sender. Thank you. >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 4 Date: Mon, 20 May 2019 18:08:34 +0000 From: "Nasiriavanaki, Zahra" <ZNASIRIAVANAKI@mgh.harvard.edu <mailto:ZNASIRIAVANAKI@mgh.harvard.edu>> Subject: Re: [Freesurfer] mkanalysis-sess refeventdur To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <DM6PR04MB44432A081ED580B5F392F5F199060@DM6PR04MB4443.namprd04.prod.outlook.com <mailto:DM6PR04MB44432A081ED580B5F392F5F199060@DM6PR04MB4443.namprd04.prod.outlook.com>> Content-Type: text/plain; charset="us-ascii" Got it. Thank you very much for your reply Mona ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> Sent: Monday, May 20, 2019 12:52:39 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mkanalysis-sess refeventdur No, you'll need to change your paradigm file to have two distinct 8 sec events rather than one 16 sec event. On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote: > > Hi Freesurfer experts > > > I am making an analysis in Freesurfer version 6 and I have a question > about the "refeventdur" in mkanalysis-sess command. > > My stimulus duration is 16 seconds, but for a specific analysis, I > only want to include half of the stimulus duration (ex: the first 8 > seconds only OR the last 8 seconds only). > > I was wondering if I can do this, by setting the "refeventdur" to 8 > seconds. Will that work? and if it does, is it including the first 8 > seconds or the last 8 seconds? > > > Thanks > > Mona > > > > *Zahra (Mona) Nasiriavanaki* > > Postdoctoral Research Fellow > > Martinos Center for Biomedical Imaging > > Massachusetts General Hospital > > 149 13th Street, 149-2615 > > Charlestown, MA, USA, 02129 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
Michal Tanzer